The free tickets did not apply to Aquatica. If you bought the 3 park annual digital San Diego pass. I didn't know Aquatica was apart of that deal. I know that Costco is selling 3 day pass tickets to Legoland, Aquatica, and the Wild Animal Park (one park per day) and they good for one year.
Pick up is at the normal ticketing desk at the park. Show your stuff and they'll give you a hard pass. As for joined aquatics passes, will have to ask sea world or aquatics. They are separate parks, but they may have a deal as they do in Florida to consolidate passes at an extra cost, though I haven't seen anything like that advertised.
Thanks! Your answer is awaiting moderation.